Warp Boxes first appear in Super Mario 3D Land. When Mario or Luigi run into a Warp Box, they are teleported to another Warp Box in another area, in a similar manner of Warp Pipes and Launch Stars. After the player comes out of a Warp Box, it may sometimes disappear, leaving Mario or Luigi with no way back.

In the early stages of the game, Warp Boxes were purple and some showed four diamonds as opposed to exclamation marks. However, the color was later given to Mystery Boxes.

Warp Boxes return in Super Mario 3D World, where they work just like they did in Super Mario 3D Land. There are also Warp Boxes that are trapped inside locked metal boxes, forcing Mario to get five Key Coins to make them available. Unlike in Super Mario 3D Land, they have the same sound effects as Mystery Boxes. When playing with multiple players, characters that do not enter the box a few seconds after one does are automatically pulled inside.